Nextflow enables reproducible computational workflows

By Paolo Di Tommaso, Maria Chatzou, Evan W. Floden, Pablo Prieto Barja, Emilio Palumbo, Cédric Notredame. Nature Biotechnology, 2017

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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation (2020, neutral): “= 1 − ;< ( >?@-;?@A B?@, >?@-;?@A B?@A ) (8) Where: • D789 and D78.”
The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024, methodology): “To enhance the robustness and efficiency of indexing biological databases required for tools such as FASTA and NCBI BLAST+, the JD data indexing pipelines were migrated to Nextflow ( 21 ).”
Segmentation of Nuclei in Histopathology Images by Deep Regression of the Distance Map (2019, methodology): “In addition, we provide nextflow scripts [50] which we use to unify the scripts in one pipeline file.”
Parsl: Pervasive Parallel Programming in Python (2019, methodology): “Scientificworkflowengines.Many workflow systems—238 at the time of writing [2]—enable the orchestrated execution of multiple applications. Examples are Pegasus [24], Galaxy [31], Swift [39], NextFlow [25], FireWorks [33], Apache Airflow [6], and Luigi [4]. Pegasus and Galaxy implement a static DAG m”
Significantly improving the quality of genome assemblies through curation (2020, neutral): “Before being loaded into gEVAL, all assemblies are run through a nextflow [39] pipeline that”
Expression Atlas update: from tissues to single cells (2019, methodology): “We currently em- ploy Nextflow at the quantification stage, and Galaxy (19) for downstream analysis in a reproducible way.”